7WIC | pdb_00007wic

Cryo-EM structure of the SS-14-bound human SSTR2-Gi1 complex

PDB DOI: https://doi.org/10.2210/pdb7WIC/pdb
EM Map EMD-32528: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus, synthetic construct
Expression System: Spodoptera frugiperda, Trichoplusia ni
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2022-01-03 Released: 2022-06-01
Deposition Author(s): Chen, L., Wang, W., Dong, Y., Shen, D., Guo, J., Qin, J., Zhang, H., Shen, Q., Zhang, Y., Mao, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structures of the endogenous peptide- and selective non-peptide agonist-bound SSTR2 signaling complexes.

Chen, L.N., Wang, W.W., Dong, Y.J., Shen, D.D., Guo, J., Yu, X., Qin, J., Ji, S.Y., Zhang, H., Shen, Q., He, Q., Yang, B., Zhang, Y., Li, Q., Mao, C.

(2022) Cell Res 32: 785-788

PubMed: 35578016 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-022-00669-z
Primary Citation Related Structures:
7WIC, 7WIG

Organizational Affiliation

Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, China.

Macromolecule Content

Total Structure Weight: 157.88 kDa
Atom Count: 9,048
Modeled Residue Count: 1,158
Deposited Residue Count: 1,421
Unique protein chains: 6

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
somatostatin-14	A [auth L]	14	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P61278 (Homo sapiens) Explore P61278 Go to UniProtKB: P61278
PHAROS: P61278 GTEx: ENSG00000157005
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61278
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Somatostatin receptor type 2	B [auth R]	369	Homo sapiens	Mutation(s): 0 Gene Names: SSTR2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P30874 (Homo sapiens) Explore P30874 Go to UniProtKB: P30874
PHAROS: P30874 GTEx: ENSG00000180616
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30874
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	C [auth A]	354	Homo sapiens	Mutation(s): 0 Gene Names: GNAI1 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	345	Rattus norvegicus	Mutation(s): 0 Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311 Go to UniProtKB: P54311
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54311
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth G]	70	Bos taurus	Mutation(s): 0 Gene Names: GNG2 Membrane Entity: Yes
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212 Go to UniProtKB: P63212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63212
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
single Fab chain (svFv16)	F [auth S]	269	synthetic construct	Mutation(s): 0

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001216 Query on PRD_001216	A [auth L]	Somatostatin-14	Cyclic peptide / Inhibitor		Interactions Focus chain A [auth L] Interactions & Density Focus chain A [auth L]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.16

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 1.1: 2022-08-17
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Refinement description, Structure summary